Gene coexpression analysis in Arabidopsis thaliana based on public microarray data

Abstract

Summary: Coexpressed genes tend to participate in related biological processes. Gene coexpression analysis allows the discovery of functional gene partners or the assignment of biological roles to genes of unknown function. In this protocol, we describe the steps necessary to create a gene coexpression tree for Arabidopsis thaliana, using publicly available Affymetrix CEL microarray data. Because the computational analysis described here is highly dependent on sample quality, we detail an automatic quality control approach.For complete details on the use and execution of this protocol, please refer to Zogopoulos et al. (2021).

Keywords

• Bioinformatics
• Genomics
• Model Organisms
• Plant sciences
• Systems biology